I can understand where he was trying to go - yes, it would be nice to see more 'real' commanders as I fly around, even as part of Mobius, it's still fairly infrequent. That said, I have no desire to PvP...I can barely hold my own against simple NPCs, let alone a fully engineered FDL...and frankly, combat isn't really the big driver for me. I do think Mobius is a symptom, not a solution...but right now, I don't see any solution in the works.
The biggest problem I see with any 'penalty system' is the availability of in-game currency. I often see/hear Commanders talking about their hundreds of millions, if not billions of credits. Hard to see how you implement a penalty structure that really punishes the guy flying his 1.2Bn-cr Cutter around blowing up people for the hell of it. 13 Million credit fine ? Peanuts...it's one trip to the ruins, maybe an hour's effort.
The only thing I could think of was some sort of bounty system that started listing the player in the mission boards as a target. The more they killed clean commanders, the higher and wider the bounty gets, and his rebuy cost is affected also (reflecting an increased insurance risk...say 30%, 60%, 100%)...so you can't just suicidwinder your way out of it. After your 3rd murder in a set time period, you no longer get insurance at all on that ship...that would make that 1.2bn cutter a juicy target for the 'good guys'...and punish the bad guy, while still leaving some leeway for the 'pirates', who generally say they only kill if the player fights back...they can run too if they can't win the fight, or let the pilot go with a hefty repair bill but without a rebuy if they don't want to incur the penalty. The insurance rebuy would slowly decay again, assuming they don't murder anyone else.
Anyway...back to work...